I have to say that despite the fact that I'm not that great at targeting the Reaper, Priority: Rannoch is my second favorite mission in the game. The Quarians are my favorite of the Mass Effect aliens and I think their history with the Geth is interesting. So I loved this and the missions where you have to save Admiral Koris and go into the Geth Consensus.
I was able to create peace between them, and that was awesome. Though if it came down to it, despite my love for Tali and the Quarians, I would have chosen the Geth. Stupid Admiral Gerral; I loved getting the option to punch him.
The mission at the Ardat-Yakishi monastery was creepy; I hate it when a Banshee screams, it really freaks me out. At this point, after having Mordin, Thane, and Legion dying it was great to have the option of preventing Samara's death.
Now on to Priority: Thessia, which I didn't like that much. I don't really like the Assari that much (mostly because it's obvious that the writers think the Assari are the best species ever) and this really made me angry with their government. You had a Protheon beacon this entire time, and you only mention it now?! Also, how the hell did no one before Shepard get information on the Reapers from it? How were the Assari able to use it to get superior technology but completely miss all the information on the Reapers? Also, the game treats losing Thessia like it's this horrible, completely disheartening loss and I didn't even come close to feeling that; at this point in the game, the Batarians are nearly extinct, Earth is being completely devestated, Palaven is on fire, so why should Thessia be this much of a loss? It's just another homeworld the Reapers have wrecked.
It was slightly improved by Javik but it still irritates me.
And Priority: Horizon was much better in my opionon. It had a creepy atmosphere even before the Husks and assorted abominations started attacking you. Henry Lawson is just as evil as Miranda described him as and I liked the scene where Miranda kills him. Miranda lived in my play-through which was nice though I wish the ME2 characters had gotten more to do in the game, particularly Thane who dies really early on.
Finally, the Cerberus Base. It was ok. My favorite part was using the really awesome Renegade Interupt to kill that glorified Nightwing cosplayer, Kai Leng. "This is for Thane, you son of a bitch."
I'll talk about my feelings about the ending and the extended cut in another post.